Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures
Abstract Background The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such as Hi-C, reveal the partitioning of chromosomes into epigenetically defined active and repressed compartments an...
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doaj-defbfc9031574c23b9197c226a472dac2021-05-11T15:00:27ZengBMCGenome Biology1474-760X2021-05-0122112010.1186/s13059-021-02343-wSuper-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structuresXian Hao0Jyotsana J. Parmar1Benoît Lelandais2Andrey Aristov3Wei Ouyang4Christian Weber5Christophe Zimmer6Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRSInstitut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRSInstitut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRSInstitut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRSInstitut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRSInstitut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRSInstitut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRSAbstract Background The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such as Hi-C, reveal the partitioning of chromosomes into epigenetically defined active and repressed compartments and smaller “topologically associated” domains. These domains are often associated with chromatin loops, which largely disappear upon removal of cohesin. Because most Hi-C implementations average contact frequencies over millions of cells and do not provide direct spatial information, it remains unclear whether and how frequently chromatin domains and loops exist in single cells. Results We combine 3D single-molecule localization microscopy with a low-cost fluorescence labeling strategy that does not denature the DNA, to visualize large portions of single human chromosomes in situ at high resolution. In parallel, we develop multi-scale, whole nucleus polymer simulations, that predict chromatin structures at scales ranging from 5 kb up to entire chromosomes. We image chromosomes in G1 and M phase and examine the effect of cohesin on interphase chromatin structure. Depletion of cohesin leads to increased prevalence of loose chromatin stretches, increased gyration radii, and reduced smoothness of imaged chromatin regions. By comparison to model predictions, we estimate that 6–25 or more purely cohesin-dependent chromatin loops coexist per megabase of DNA in single cells, suggesting that the vast majority of the genome is enclosed in loops. Conclusion Our results provide new constraints on chromatin structure and showcase an affordable non-invasive approach to study genome organization in single cells.https://doi.org/10.1186/s13059-021-02343-wChromatinChromosomesCohesinSuper-resolution microscopyPolymer models |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xian Hao Jyotsana J. Parmar Benoît Lelandais Andrey Aristov Wei Ouyang Christian Weber Christophe Zimmer |
spellingShingle |
Xian Hao Jyotsana J. Parmar Benoît Lelandais Andrey Aristov Wei Ouyang Christian Weber Christophe Zimmer Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures Genome Biology Chromatin Chromosomes Cohesin Super-resolution microscopy Polymer models |
author_facet |
Xian Hao Jyotsana J. Parmar Benoît Lelandais Andrey Aristov Wei Ouyang Christian Weber Christophe Zimmer |
author_sort |
Xian Hao |
title |
Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures |
title_short |
Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures |
title_full |
Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures |
title_fullStr |
Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures |
title_full_unstemmed |
Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures |
title_sort |
super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures |
publisher |
BMC |
series |
Genome Biology |
issn |
1474-760X |
publishDate |
2021-05-01 |
description |
Abstract Background The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such as Hi-C, reveal the partitioning of chromosomes into epigenetically defined active and repressed compartments and smaller “topologically associated” domains. These domains are often associated with chromatin loops, which largely disappear upon removal of cohesin. Because most Hi-C implementations average contact frequencies over millions of cells and do not provide direct spatial information, it remains unclear whether and how frequently chromatin domains and loops exist in single cells. Results We combine 3D single-molecule localization microscopy with a low-cost fluorescence labeling strategy that does not denature the DNA, to visualize large portions of single human chromosomes in situ at high resolution. In parallel, we develop multi-scale, whole nucleus polymer simulations, that predict chromatin structures at scales ranging from 5 kb up to entire chromosomes. We image chromosomes in G1 and M phase and examine the effect of cohesin on interphase chromatin structure. Depletion of cohesin leads to increased prevalence of loose chromatin stretches, increased gyration radii, and reduced smoothness of imaged chromatin regions. By comparison to model predictions, we estimate that 6–25 or more purely cohesin-dependent chromatin loops coexist per megabase of DNA in single cells, suggesting that the vast majority of the genome is enclosed in loops. Conclusion Our results provide new constraints on chromatin structure and showcase an affordable non-invasive approach to study genome organization in single cells. |
topic |
Chromatin Chromosomes Cohesin Super-resolution microscopy Polymer models |
url |
https://doi.org/10.1186/s13059-021-02343-w |
work_keys_str_mv |
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1721443809345142784 |